基于模糊谱聚类的不确定蛋白质相互作用网络功能模块挖掘

针对谱聚类融合模糊C-means（FCM）聚类的蛋白质相互作用（PPI）网络功能模块挖掘方法准确率不高、执行效率较低和易受假阳性影响的问题，提出一种基于模糊谱聚类的不确定PPI网络功能模块挖掘（FSC-FM）方法。首先，构建一个不确定PPI网络模型，使用边聚集系数给每一条蛋白质交互作用赋予一个存在概率测度，克服假阳性对实验结果的影响；第二，利用基于边聚集系数流行距离（FEC）策略改进谱聚类中的相似度计算，解决谱聚类算法对尺度参数敏感的问题，进而利用谱聚类算法对不确定PPI网络数据进行预处理，降低数据的维数，提高聚类的准确率；第三，设计基于密度的概率中心选取策略（DPCS）解决模糊C-means算法对初始聚类中心和聚类数目敏感的问题，并对预处理后的PPI数据进行FCM聚类，提高聚类的执行效率以及灵敏度；最后，采用改进的边期望稠密度（EED）对挖掘出的蛋白质功能模块进行过滤。在酵母菌DIP数据集上运行各个算法可知，FSC-FM与基于不确定图模型的检测蛋白质复合物（DCU）算法相比，F-measure值提高了27.92%，执行效率提高了27.92%；与在动态蛋白质相互作用网络中识别复合物的方法（CDUN）、演化算法（EA）、医学基因或蛋白质预测算法（MGPPA）相比也有更高的F-measure值和执行效率。实验结果表明，在不确定PPI网络中，FSC-FM适合用于功能模块的挖掘。     

Backtesting portfolio value-at-risk with estimated portfolio weights

This article theoretically and empirically analyzes backtesting portfolio value-at-risk (VaR) with estimation risk in an intrinsically multi-variate framework. It particularly takes into account the estimation of portfolio weights in forecasting portfolio VaR and its impact on backtesting. It shows that the estimation risk from estimating portfolio weights and that from estimating the multi-variate dynamic model make the existing methods in a univariate framework inapplicable. It proposes a general theory to quantify estimation risk applicable to the present problem and suggests practitioners a simple but effective way to implement valid inference to overcome the effect of estimation risk in backtesting portfolio VaR. In particular, we apply our theory to the efficient mean-variance-skewness portfolio for a multi-variate generalized autoregressive conditional heteroscedasticity model with multi-variate general hyperbolic distributed innovations. Some Monte Carlo simulations and an empirical application demonstrate the merits of our method.     

A web-based software tool for participatory optimization of conservation practices in watersheds

WRESTORE (Watershed Restoration Using Spatio-Temporal Optimization of Resources) is a web-based, participatory planning tool that can be used to engage with watershed stakeholder communities, and involve them in using science-based, human-guided, interactive simulation–optimization methods for designing potential conservation practices on their landscape. The underlying optimization algorithms, process simulation models, and interfaces allow users to not only spatially optimize the locations and types of new conservation practices based on quantifiable goals estimated by the dynamic simulation models, but also to include their personal subjective and/or unquantifiable criteria in the location and design of these practices. In this paper, we describe the software, interfaces, and architecture of WRESTORE, provide scenarios for implementing the WRESTORE tool in a watershed community's planning process, and discuss considerations for future developments.     

Managing readiness-relevant activities for the organizational dimension of ERP implementation

An organization requires performing readiness-relevant activities to ensure successful implementation of an enterprise resource planning (ERP) system. This paper develops a novel approach to managing these interrelated activities to get ready for implementing an ERP system. The approach enables an organization to evaluate its ERP implementation readiness by assessing the degree to which it can achieve the interrelated readiness relevant activities using fuzzy cognitive maps. Based on the interrelationship degrees among the activities, the approach clusters the activities into manageable groups and prioritizes them. To help work out a readiness improvement plan, scenario analysis is conducted.     

优化军工科研项目管理的具体策略

我国的军工科研所成立于上世纪，它以军工项目的科研、预研为主，为我国的国防军工提供研发产品。伴随着我国经济实力的增强和科技军事力量的增长，军工科研院所也转变了原有的工业专属性质，走上了军民两用、寓军于民的道路，并在时代的进步中成为了我国先进装备制造业的重要科研力量和科技创新支柱。凸现军事工业“高、精、尖”的特点，以项目管理的优化为具体策略进行军工科研开发工作。     

基于MF-R和AWS密钥管理机制的物联网健康监测大数据分析系统

带有传感器的可穿戴式医疗设备不断生成大量数据，由于数据的复杂性，难以通过处理和分析大数据来找到有价值的决策信息。为了解决这个问题，提出了一种新的物联网体系结构，用于存储和处理医疗应用的可扩展传感器数据（大数据）。所提出的架构主要由两个子架构组成：Meta Fog重定向（MF-R）架构和AWS密钥管理机制。MF-R架构使用Apache Pig和Apache HBase等大数据技术来收集和存储不同传感器设备生成的传感器数据，并利用卡尔曼滤波消除噪声。AWS密钥管理机制使用密钥管理方案，目的是保护云中的数据，防止未经授权的访问。当数据存储在云中时，所提出的系统能够使用随机梯度下降算法和逻辑回归来开发心脏病的预测模型。仿真实验表明，和其他几种算法相比，提出的算法具有更小的误差，且在吞吐量、准确度等方面具有一定的优越性。     

Automated network management and configuration using Probabilistic Trans-Algorithmic Search

Online configuration of large-scale systems such as networks requires parameter optimization within a limited amount of time, especially when configuration is needed as a response to recover from a failure in the system. To quickly configure such systems in an online manner, we propose a Probabilistic Trans-Algorithmic Search (PTAS) framework which leverages multiple optimization search algorithms in an iterative manner. PTAS applies a search algorithm to determine how to best distribute available experiment budget among multiple optimization search algorithms. It allocates an experiment budget to each available search algorithm and observes its performance on the system-at-hand. PTAS then probabilistically reallocates the experiment budget for the next round proportional to each algorithm’s performance relative to the rest of the algorithms. This “roulette wheel” approach probabilistically favors the more successful algorithm in the next round. Following each round, the PTAS framework “transfers” the best result(s) among the individual algorithms, making our framework a trans-algorithmic one. PTAS thus aims to systematize how to “search for the best search” and hybridize a set of search algorithms to attain a better search. We use three individual search algorithms, i.e., Recursive Random Search (RRS) (Ye and Kalyanaraman, 2004), Simulated Annealing (SA) (Laarhoven and Aarts, 1987), and Genetic Algorithm (GA) (Goldberg, 1989), and compare PTAS against the performance of RRS, GA, and SA. We show the performance of PTAS on well-known benchmark objective functions including scenarios where the objective function changes in the middle of the optimization process. To illustrate applicability of our framework to automated network management, we apply PTAS on the problem of optimizing link weights of an intra-domain routing protocol on three different topologies obtained from the Rocketfuel dataset. We also apply PTAS on the problem of optimizing aggregate throughput of a wireless ad hoc network by tuning datarates of traffic sources. Our experiments show that PTAS successfully picks the best performing algorithm, RRS or GA, and allocates the time wisely. Further, our results show that PTAS’ performance is not transient and steadily improves as more time is available for search.     

A two stage heuristic algorithm for the integrated aircraft and crew schedule recovery problems

Airline disruptions incurred huge cost for airlines and serious inconvenience for travelers. In this paper, we study the integrated aircraft and crew schedule recovery problem. A two stage heuristic algorithm for the integrated recovery problem is proposed. In the first stage, the integrated aircraft recovery and flight-rescheduling model with partial crew consideration is built. This model is based on the traditional multi-commodity network model for the aircraft schedule recovery problem. The objective of this model also includes minimization of the original crew connection disruption. In the second stage, the integrated crew schedule recovery and flight re-scheduling model with partial aircraft consideration is built. We proposed a new multi-commodity model for the crew schedule recovery. The main advantage of such model is that it is much more efficient to integrate the flight-scheduling and aircraft consideration. New constraints are incorporated to guarantee that the aircraft connections generated in the stage 1 are still feasible. Two stages are run iteratively until no improvement can be achieved. Experimental results show that our method can provide better recovery solutions compared with the benchmark algorithms.     

Characterizing physical habitat preferences and thermal refuge occupancy of brook trout (Salvelinus fontinalis) and Atlantic salmon (Salmo salar) at high river temperatures

Anthropogenic influences, including climate change, are increasing river temperatures in northern and temperate regions and threatening the thermal habitats of native salmonids. When river temperatures exceed the tolerance levels of brook trout and Atlantic salmon, individuals exhibit behavioural thermoregulation by seeking out cold‐water refugia – often created by tributaries and groundwater discharge. Thermal infrared (TIR) imagery was used to map cold‐water anomalies along a 53 km reach of the Cains River, New Brunswick. Trout and salmon parr did not use all identified thermal anomalies as refugia during higher river temperature periods (>21°C). Most small‐bodied trout (8–30 cm) were observed in 80% of the thermal anomalies sampled. Large‐bodied trout (>35 cm) required a more specific set of physical habitat conditions for suitable refugia, that is, 100% of observed large trout used 30% of the anomalies sampled and required water depths >65 cm within or adjacent to the anomaly. Densities of trout were significantly higher within anomalies compared with areas of ambient river temperature. Salmon parr were less aligned with thermal anomalies at the observed temperatures, that is, 59% were found in 65% of the sampled anomalies; and densities were not significantly different within/ outside anomalies. Salmon parr appeared to aggregate at 27°C, and after several events over 27°C variability in aggregation behaviour was observed – some fish aggregated at 25°C, others did not. We stipulate this is due to variances of thermal fatigue. Habitat suitability curves were developed for velocity, temperature, depth, substrate, and deep water availability to characterize conditions preferred by fish during high‐temperature events. These findings are useful for managers as our climate warms, and can potentially be used as a tool to help conserve and enhance thermal refugia for brook trout and Atlantic salmon in similar systems.     

Evaluation of expanded gamut software solutions for spot color reproduction

Expanded gamut printing is an approach in color reproduction that expands the color gamut of conventional CMYK printing processes via the use of additional colorants, such as Orange, Green, and Violet inks. This study evaluates the ability of commercial color management software to create an accurate solution for an expanded gamut printing system. In this study, two printing processes were used, an Epson SureColor P9000 inkjet printer/proofer and an HP Indigo 7900 digital production press, both with 7-color expanded gamut ink sets. Software solutions from Alwan, CGS ORIS, ColorLogic, GMG Color, Heidelberg, and Kodak were evaluated. The systems were tested to see how well they could reproduce the colors in the entire PANTONE+ Solid Coated spot color library. It is shown that the solutions are able to reproduce 89% to 94% of the spot colors on the Epson P9000 inkjet printer and 77% to 87% of the library on the Indigo 7900, both to less than two CIEDE2000 (a typical tolerance in label and packaging work). The number of color patches in expanded gamut characterization test charts was noted, as this is still an area of proprietary, nonstandardized working practice. There are many different colorant combinations that can make the same color in expanded gamut printing. The ink build created by the different software solutions was studied, as it relates to press stability through appropriate choice of colorants. Pantone and Adobe provide everyday commercial tools for expanded color workflows. The study identified some issues with products from these companies that could confuse a less-skilled user in a busy production environment. The conclusion of the study is that expanded gamut solutions for spot color printing produce totally acceptable results for digital printing processes; expanded gamut printing is ready, here and now. The findings show that expanded gamut printing can replace cumbersome conventional spot color workflows creating considerable savings and advantages, especially for label and packaging printers.